Cornous Biology, Volume 1, Issue 1 : 7-17. Doi : 10.37446/corbio/ra/1.1.2023.7-17
Review Article

OPEN ACCESS | Published on : 30-Jun-2023

Genome editing for enhancing abiotic stress tolerance in crop plants

  • Sivaji Mathivanan
  • Agricultural Biotechnology, Agricultural College and Research Institute(AC&RI), TNAU, Vazhavachanur, Tiruvannamalai, Tamil Nadu, India.
  • Shakespear Sundaresan
  • Plant Biotechnology, ICAR-National Institute of Biotic Stress Management, Baronda, Raipur (CG), India.
  • Chandrasekar Arumugam
  • Assistant Professor (Biotechnology), Department of Crop Improvement, SRM College of Agricultural Sciences, Vendhar Nagar, Baburayanpettai, Tamil Nadu, India.


The globe has to treble the crop production rates in order to improve food security for future generations. However, crop production would likely become more challenging in the future since current crop types and crop development techniques might not be strong enough to withstand the rising abiotic pressures brought on by climate change. The primary cause of crop loss worldwide is abiotic stress, which reduces average yields for the majority of agricultural crops i.e., by more than 50%. The main environmental stresses that reduce crop production and productivity are drought, salinity, extreme temperatures, and cold. Crop improvement is the key element for the sustainable food production and modern crop improvement methods are very proficient that achieve remarkable improvements in plant performance against abiotic stress. One of the most important modern crop improvement method is genome editing. The advent of genome editing has generated a lot of excitement, especially among agricultural scientists, because it offers new chances to create improved crop varieties with the precise addition of beneficial traits. Genome editing is like mutational breeding; through this method, that is possible to create targeted genome modification and also possible to improve crop varieties with enhanced abiotic stress resistance. This review briefly discusses abiotic stress, genome editing, mechanisms, different types and applications in crop improvement against abiotic resistance.


CRISPR/Cas9, crop improvement, abiotic stress, tolerance, genome editing, rice


  • Ahmad, P., Tripathi, D.K., Deshmukh, R., Pratap Singh, V. & Corpas, F.J. (2019). Revisiting the Role of ROS and RNS in Plants under Changing Environment; Elsevier: Amsterdam, The Netherlands.

    Alfatih, A., Wu, J., Jan, S.U., Zhang, Z.S., Xia, J.Q. & Xiang, C.B. (2020). Loss of rice PARAQUAT TOLERANCE 3 confers enhanced resistance to abiotic stresses and increases grain yield in field. Plant Cell Environ., 43, 2743–2754.

    Aziz, K., Daniel, K.Y.T., Muhammad, Z.A., Honghai, L., Shahbaz, A.T., Mir, A. & Fahad, S.  Nitrogen fertility and abiotic stresses management in cotton crop: a review. (2017). Environ. Sci. Pollut. Res., 24, 14551–14566.

    Beck, E.H., Fettig S., Knake C., Hartig K. & Bhattarai T. (2007). Specific and Unspecific Responses of Plants to Cold and Drought Stress. Journal Biosciences, 32(3), 501–510.

    Bhat, J.A., Deshmukh, R., Zhao, T., Patil, G., Deokar, A., Shinde, S. & Chaudhary, J. (2020). Harnessing high-throughput phenotyping and genotyping for enhanced drought tolerance in crop plants. J. Biotechnol., 324, 248–260.

    Bo, W., Zhaohui, Z., Huanhuan, Z., Xia, W., Binglin, L., Lijia, Y., Xiangyan, H., Deshui, Y., Xuelian, Z. & Chunguo, W. (2019). Targeted Mutagenesis of NAC Transcription Factor Gene, OsNAC041, Leading to Salt Sensitivityin Rice. Rice Sci., 26, 98–108.

    Boudsocq, M., & Lauriere, C. (2005). Osmotic Signaling in Plants: Multiple Pathways Mediated by Emerging Kinase Families. Plant Physiology, 138(3), 1185–1194.

    Campa, C.C., Weisbach, N.R., Santinha, A.J. Incarnato, D. & Platt, R. (2019). Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nat. Methods.  16, 887–893.

    Cramer G.R.,  Urano  K.,  Delrot S.,  Pezzotti M. & Shinozaki. K. (2011). Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol., 11, 163-176.

    Deriano, L. & Roth, D.B. (2013). Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. Annual Review of Genetics, 47 (1), 433–455.

    Fedoroff,  N.V., Battisti, D.S., Beachy, R.N., Cooper, P.J., Fischhoff, D.A., Hodges, C.N., Knauf, V.C., Lobell, D., Mazur, B.J. & Molden, D. (2010). Radically rethinking agriculture for the 21st century. Science, 327, 833-834. 

    Gasiunas, G.,  Barrangou, R., Horvath, P. & Siksnys, V. (2012). Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences, 109(39), 2579–2586,

    Gilmour, S.J., Zarka, D.G., Stockinger, E.J., Salazar, M.P., Houghton, J.M. & Thomashow M.F. (1998).  Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold induced COR gene expression. The Plant Journal, 16, 433– 442.

    Guo, X., Liu, D. & Chong, K. (2018). Cold signaling in plants: Insights into mechanisms and regulation. J. Integr. Plant Biol. 60, 745–756.

    Han, X., Chen, Z., Li, P., Xu, H., Liu, K., Zha, W., Li, S., Chen, J., Yang, G., Huang, J. & et al. (2022). Development of novel rice germplasm for salt-tolerance at seedling stage using CRISPR-Cas9. Sustainability, 14, 2621.

    Hesham, F.A. & Fahad, S. (2020). Melatonin application enhances biochar efficiency for drought tolerance in maize varieties: Modifications in physio-biochemical machinery. Agron J., 1–22.

    Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q. & Xiong, L. (2006). Overexpressing a NAM, ATAF, and CUC (NAC) Transcription Factor Enhances Drought Resistance and Salt Tolerance in Rice. Proceedings of the National Academy of Sciences, 103(35), 12987– 12992.

    Illouz-Eliaz, N., Nissan, I., Nir, I., Ramon, U., Shohat, H. & Weiss, D. (2020). Mutations in the tomato gibberellin receptors suppress xylem proliferation and reduce water loss under water-deficit conditions. J. Exp. Bot., 71, 3603–3612.

    Jia, Y.X.,  Ding, Y.L., Shi, Y.T., Zhang, X.Y., Gong, Z.Z. & Yang, S.H. (2016). The cbfs triple mutants reveal the essential functions of CBFs in cold acclimation and allow the definition of CBF regulons in Arabidopsis. New Phytologist,  212, 345– 353.

    Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A. & Charpentier, E. (2012). A programmable dual-RNA guided DNA endonuclease in adaptive bacterial immunity. Science, 337,  6096,  816–821.

    Joung, J.K.  & Sander, J.D. (2013). TALENs: a widely applicable technology for targeted genome editing. Nature Reviews, Molecular Cell Biology, 14, 1, 49–55,

    Kazuko, Y.S. & Shinozaki K. (2006). Transcriptional Regulatory Networks in Cellular Responses and Tolerance to Dehydration and Cold Stresses. Annual Review of Plant Biology, 57, 781-803.

    Kundzewicz, Z., Ulbrich, U.,  Brucher, T., Graczyk, D.,  Kruger, A. & Leckebusch G.C. (2005). Summer floods in central Europe-climate change track? Nat. Hazar, 36, 165-189.

    Lan, T., Zheng, Y., Su, Z., Yu, S., Song, H., Zheng, X., Lin, G. & Wu, W. (2019). OsSPL10, a SBP-Box gene, plays a dual role in salt tolerance and trichome formation in rice (Oryza sativa L.). G3,  9:4107–4114.

    Li, X., Xu, S., Fuhrmann-Aoyagi, M.B., Yuan, S., Iwama, T., Kobayashi, M. & Miura, K. (2022). CRISPR/Cas9 Technique for Temperature, Drought, and Salinity Stress Responses. Curr. Issues Mol. Biol., 44, 2664–2682.

    Liao, S. Qin, X. Luo, L. Han, Y. Wang, X. Usman, B. Nawaz, G. Zhao, N. Liu, Y. & Li, R. (2019). CRISPR/Cas9-induced mutagenesis of semi-rolled leaf1, 2 confers curled leaf phenotype and drought tolerance by influencing protein expression patterns and ROS scavenging in rice (Oryza sativa L.). Agronomy, 9, 728.

    Liu, L., Zhang, J., Xu, J., Li, Y., Guo, L., Wang, Z., Zhang, X., Zhao, B., Guo, Y.D. & Zhang, N. (2020). CRISPR/Cas9 targeted mutagenesis of SlLBD40, a lateral organ boundaries domain transcription factor, enhances drought tolerance in tomato. Plant Sci., 301,110683.

    Liu, Q., Kasuga, M., Sakuma, Y., Abe, H. and Miura S., Yamaguchi-Shinozaki K. & Shinozaki K.  (1998). Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought and low temperature responsive gene expression, respectively, in ArabidopsisPlant Cell, 10, 1391– 1406.

    Liu, S., Li, C., Wang, H., Wang, S., Yang, S., Liu, X., Yan, J., Li, B., Beatty, M. & Zastrow-Hayes, G. (2020). Mapping regulatory variants controlling gene expression in drought response and tolerance in maize. Genome Biol., 21, 163.

    Liu, S., Li, C., Wang, H., Wang, S., Yang, S., Liu, X., Yan, J., Li, B., Beatty, M., Zastrow-Hayes, G. & et al. (2020). Mapping regulatory variants controlling gene expression in drought response and tolerance in maize. Genome Biol., 21,163.

    Ma, X., Zhu, Q., Chen, Y. & Liu, Y.G. (2016). CRISPR/Cas9 platforms for genome editing in plants: developments and applications. Molecular Plant, 9 (7), 961–974.

    Marques S.J. & Arrabaca M.C. (2004). Contributions of soluble carbohydrates to the osmotic adjustment in the C4 grass setarias phacelata: a comparison between rapidly and slowly imposed water stress. Journal of Plant Physiology, 161(5), 551-555.

    Mathivanan, S. (2021). Abiotic stress-induced molecular and physiological changes and adaptive mechanisms in plants. abiotic stress in plants, IntechOpen, doi:10.5772/intechopen.93367.

    Mian, A., Oomen, R.J., Isayenkov, S., Sentenac, H., Maathuis, F.J. & Very, A.A. (2011). Over-expression of a Na+-and K+-permeable HKT transporter in barley improves salt tolerance. Plant J., 68, 468–479.

    Miller, J.C., Tan, S., Qiao, G. & et al., 2011. A TALE nuclease architecture for efficient genome editing.  Nature Biotechnology, 29 (2), 143–148.

    Munns, R. & Tester, M. (2008). Mechanisms of salinity tolerance. Annu. Rev. Plant Biol., 59, 651.

    Mushtaq, M., Bhat, J.A., Mir, Z.A., Sakina, A., Ali, S. Singh, A.K., Tyagi, A., Salgotra, R.K., Dar, A.A. & Bhat, R. (2018). CRISPR/Cas approach: A new way of looking at plant-abiotic interactions. J. Plant Physiol., 224, 156–162.

    Nawaz, G., Han, Y., Usman, B., Liu, F., Qin, B. &  Li, R. (2019). Knockout of OsPRP1, a gene encoding proline-rich protein, confers enhanced cold sensitivity in rice (Oryza sativa L.) at the seedling stage. Biotech, 9, 254.

    Nunez-Munoz, L., Vargas-Hernandez, B., Hinojosa-Moya, J., Ruiz-Medrano, R. & Xoconostle-Cazares, B. (2021). Plant drought tolerance provided through genome editing of the trehalase gene. Plant Signal. Behav. 16, 1877005.

    Ogata, T., Ishizaki, T., Fujita, M. & Fujita, Y. (2020). CRISPR/Cas9-targeted mutagenesis of OsERA1 confers enhanced responses to abscisic acid and drought stress and increased primary root growth under nonstressed conditions in rice. PLoS ONE, 15, 0243376.

    Orvar, B.L, Sangwan, V., Omann, F. & Dhindsa, R.S. (2000). Early steps in cold sensing by plant cells: the role of actin cytoskeleton and membrane fluidity. The Plant Journal, 23, 785–794.

    Osakabe, Y. & Osakabe, K. (2015). Genome editing with engineered nucleases in plants. Plant and Cell Physiology, 56 (3), 389–400.

    Osakabe, Y. & Osakabe, K. (2017). Genome Editing to Improve Abiotic Stress Responses in Plants. In Progress in Molecular Biology and Translational Science; Elsevier: Amsterdam, The Netherlands, 149, 99–109.

    Osakabe, Y., Watanabe, T., Sugano, S. S., Ueta, R., Ishihara, R., Shinozaki, K. & et al. (2016). Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Sci. Rep. 6, 26685. doi: 10.1038/srep26685.

    Park, J.J., Dempewolf, E., Zhang, W. & Wang, Z.Y. (2017). RNA-guided transcriptional activation via CRISPR/dCas9 mimics overexpression phenotypes in Arabidopsis. PLoS ONE, 12, e0179410.

    Piatek, A., Ali, Z., Baazim, H., Li, L., Abulfaraj,  A. & Al-Shareef,  S. (2015). RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnology, 13, 578–589.

    Que, Z., Lu, Q., Liu, T., Li, S., Zou, J. & Chen, G. (2020). The rice annexin gene OsAnn5 is a positive regulator of cold stress tolerance at the seedling stage. Res. Sq.; in press.

    Rath, D., Amlinger, L., Rath, A. & Lundgren, M. (2015). The CRISPR-Cas immune system: biology, mechanisms and applications, Biochimie, 117, 119–128.

    Roca Paixao, J.F., Gillet, F.X., Ribeiro, T.P., Bournaud, C., Lourenco-Tessutti, I.T., Noriega, D.D., Melo, B.P., de Almeida-Engler, J. & Grossi-de-Sa, M.F. (2019). Improved drought stress tolerance in Arabidopsis by CRISPR/dCas9 fusion with a Histone Acetyl Transferase. Sci. Rep., 9, 8080.

    Ruelland, E., Vaultier, M.N., Zachowski, A. &  Hurry V.  (2009). Cold signalling and cold acclimation in plants. Advances in Botanical Research., 49, 35–150.

    Sanghera, G.S., Wani, S.H., Hussain, W. & Singh, N. (2011). Engineering cold stress tolerance in crop plants. Curr. Genom., 12, 30.

    Shakesphere, S., Sivaji, M. & Sathish raj, R.  (2022). Promises and Potentiality of Genome Editing in Crop Improvement. Vijyan Varta, 3 (7), 80-86.

    Shen, C., Que, Z., Xia, Y., Tang, N., Li, D., He, R. & Cao, M. (2017). Knock out of the annexin gene OsAnn3 via CRISPR/Cas9-mediated genome editing decreased cold tolerance in rice. J. Plant Biol., 60, 539–547.

    Shi, J., Gao, H., Wang, H., Lafitte, H.R., Archibald, R.L., Yang, M., Hakimi, S.M., Mo, H., & Habben, J.E. (2017). ARGOS 8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol. J., 15, 207–216.

    Siddiqui, K.S. &  Cavicchioli, R. (2006). Cold‐adapted enzymes. Annual Review of Biochemistry, 75, 403– 433.

    Stockinger, E.J., Gilmour, S.J. & Thomashow, M.F.  (1997). Arabidopsis thaliana CBF1 encodes an AP2 domain containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proceedings of the National Academy of Sciences,  94, 1035– 1040.

    Suzuki, S., Ohta, K., Nakajima Y. & et al., 2020. Meganuclease-based artificial transcription factors, ACS Synthetic Biology, 9 (10), 2679–2691.

    Tran, M.T., Doan, D.T.H., Kim, J., Song, Y.J., Sung, Y.W., Das, S., Kim, E.J., Son, G.H., Kim, S.H. & Van Vu, T. (2021). CRISPR/Cas9-based precise excision of SlHyPRP1 domain (s) to obtain salt stress-tolerant tomato. Plant Cell Rep., 40, 999–1011.

    Vishwakarma, K., Mishra, M., Patil, G., Mulkey, S., Ramawat, N., Pratap Singh, V., Deshmukh, R., Kumar Tripathi, D., Nguyen, H.T. & Sharma, S. (2019). Avenues of the membrane transport system in adaptation of plants toabiotic stresses. Crit. Rev. Biotechnol., 39, 861–883.

    Volkov, V. (2015). Salinity tolerance in plants. Quantitative approach to ion transport starting from halophytes and stepping to genetic and protein engineering for manipulating ion fluxes. Front. Plant Sci., 6, 873.

    Voytas, D.F. (2013). Plant genome engineering with sequence specific nucleases. Annu. Rev. Plant Biol. 64, 327–350.

    Wang, L., Zhao, R., Zheng, Y., Chen, L., Li, R., Ma, J. Hong, X., Ma, P., Sheng, J. & Shen, L. (2017). SlMAPK1/2/3 and antioxidant enzymes are associated with H2O2-induced chilling tolerance in tomato plants. J. Agric. Food Chem., 65, 6812–6820.

    Wang, T., Xun, H., Wang, W., Ding, X., Tian, H., Hussain, S., Dong, Q., Li, Y., Cheng, Y., Wang, C. & et al. (2021). Mutation of GmAITR genes by CRISPR/Cas9 genome editing results in enhanced salinity stress tolerance in soybean. Front. Plant Sci., 12.

    Wang, W.C., Lin, T.C., Kieber, J. & Tsai, Y.C. (2019). Response Regulators 9 and 10 negatively regulate salinity tolerance in rice. Plant Cell Physiol., 60, 2549–2563.

    Wang, Y., Cao, Y., Liang, X. & et al. (2022). A dirigent family protein confers variation of Casparian strip thickness and salt tolerance in maize. Nat. Commun., 13, 2222.

    Wang, Y., Cheng, X., Shan, Q., Zhang, Y., Liu, J. & Gao, C. (2014). Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat. Biotechnol., 32, 947–951.

    Wu, J., Yan, G., Duan, Z., Wang, Z., Kang, C., Guo, L. &  et al. (2020). Roles of the Brassica napus DELLA protein BnaA6. RGA, in modulating drought tolerance by interacting with the ABA signaling component BnaA 10. ABF2. Front. Plant Sci., 11. doi: 10.3389/fpls.2020.00577.

    Xiong, L., Schumaker, K.S., & Zhu J.K. (2002). Cell Signaling during cold, drought, and salt stress. The Plant Cell., 165-83.

    Yadav, S. Cold stress tolerance mechanisms in plants. A review. (2010). Agron. Sustain. Dev., 30, 515–527.

    Yamaguchi & Shinozaki K.  (1994). A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell, 6, 251– 264.

    Yang, W., Chen, S., Cheng, Y., Zhang, N., Ma, Y.,Wang, W., Tian, H., Li, Y., Hussain, S., & Wang, S. (2020). Cell wall/vacuolar inhibitor of fructosidase 1 regulates ABA response and salt tolerance in Arabidopsis. Plant Signal. Behav., 15,1744293.

     Yu, J., Ge, H., Wang, X., Tang, R., Wang, Y., Zhao, F., Lan, W., Luan S. and Yang, L. (2017). Overexpression of pyrabactin resistance-like abscisic acid receptors enhances drought, osmotic, and cold tolerance in transgenic poplars. Front Plant Sci., 8, 1752. 3389/fpls.2017.01752

    Yue, E. Cao, H. & Liu, B. (2020). OsmiR535, a potential genetic editing target for drought and salinity stress tolerance in Oryza sativa. Plants,  9, 1337.

    Yue, Y., Zhang, M., Zhang, J., Duan, L. & Li, Z. (2012). SOS1 gene overexpression increased salt tolerance in transgenic tobacco by maintaining a higher K+/Na+ ratio. J. Plant Physiol., 169, 255–261.

    Zargar, S.M., Nagar, P., Deshmukh, R., Nazir, M., Wani, A.A., Masoodi, K.Z., Agrawal, G.K. and Rakwal, R. (2017). Aquaporins as potential drought tolerance inducing proteins: Towards instigating stress tolerance. J. Proteom., 169, 233–238.

     Zeng, Y., Wen, J., Zhao, W., Wang, Q. and Huang, W. (2020). Rational improvement of rice yield and cold tolerance by editing the three genes OsPIN5b, GS3, and OsMYB30 with the CRISPR–Cas9 system. Front. Plant Sci., 10, 1663.

    Zhang, A., Liu, Y., Wang, F., Li, T., Chen, Z., Kong, D. Bi, J., Zhang, F., Luo, X. and Wang, J. (2019). Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene. Mol. Breed., 39, 47.

    Zhang, A., Liu, Y., Wang, F., Li, T., Chen, Z., Kong, D., Bi, J., Zhang, F., Luo, X., Wang, J., et al. (2019). Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene. Mol. Breed., 39, 47.

    Zhang, H. Zhang, J. Wei, P.  Zhang, B.  Gou, F. Feng, Z.  Mao, Y.  Yang, L.  Zhang, H.  Xu, N. et al. (2014). The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol. J. 12, 797–807.

    Zhang, X., Fowler, S.G., Cheng, H.M., Lou, Y.G., Rhee, S.Y., Stockinger, E.J. and Thomashow M.F. (2004). Freezing sensitive tomato has a functional CBF cold response pathway, but a CBF regulon that differs from that of freezing tolerant ArabidopsisThe Plant Journal, 39, 905– 919.

    Zhao, C.Z., Zhang, Z.J, Xie, S.J, Si, T., Li, Y.Y. & Zhu, J.K. (2016). Mutational evidence for the critical role of CBF transcription factors in cold acclimation in ArabidopsisPlant Physiology.,  171, 2744– 2759.

     Zhao, Y., Zhang, C., Liu,W., Gao,W., Liu, C., Song, G., Li, W.X., Mao, L., Chen, B. & Xu, Y. (2016). An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci. Rep., 6, 23890.

    Zhu, L.,  Chen, S.,  Alvarez, S.,  Asirvatham, V.S.,  Schachtman, D.P. &  Wu Y. (2006). Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water soluble and lightly ionically bound proteins. Plant Physiol., 140,  311-325.